In sedimentary basins, deep-seated overpressure conditions are frequently encountered. However, the precise origins of these overpressure conditions and the assessment of their formation times have long presented challenges. Previous studies have primarily relied on qualitative approaches to investigate overpressure origins, leading to substantial uncertainties in their findings. Based on theories such as the effective stress law, disequilibrium compaction, equilibrium depth, and nested fluid trapping containers in this paper, a new quantitative methodology is introduced for identifying the disequilibrium-compaction-induced origins of overpressure conditions. Additionally, the formation times of overpressure can be also estimated by nested fluid trapping container theory. This methodology is successfully applied to the northwestern Bozhong subbasin in the Bohai Bay Basin, China. The results indicate that the overpressure within the Dongying Formation of the northwestern Bozhong subbasin is primarily attributed to the disequilibrium compaction of mudstone, because the disequilibrium compaction of mudstone accounts for over 90% of the pressure in sandstone. Furthermore, the overpressure system in this area is not singular but comprises multiple nested relative fluid trapping containers. The application of nested fluid trapping container theory allows for an estimation of the overpressure’s formation time, although further validation of these estimates is required. It should be noted that the method proposed in this paper is particularly suited for sedimentary basins with relatively weak tectonic activity.